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Detailed information for vg0625534713:

Variant ID: vg0625534713 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25534713
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.27, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTTCCAAAAGGTTCTGATAAACGACGATTTGGGCGGAGTCGCGACACAAATCGATCTGGCTTCTTGAACGCGCACGCTCTTGAGCCCTGCAATCGCAG[T/C]
ATCACGTCTCCTCTGGTTATCACCCGTGTCGAAACGCGGATGACCTCGCCGAGAAGGCTAATCCCTATTTGCCAATCGAAGAACACAAACAAGAACGAGA

Reverse complement sequence

TCTCGTTCTTGTTTGTGTTCTTCGATTGGCAAATAGGGATTAGCCTTCTCGGCGAGGTCATCCGCGTTTCGACACGGGTGATAACCAGAGGAGACGTGAT[A/G]
CTGCGATTGCAGGGCTCAAGAGCGTGCGCGTTCAAGAAGCCAGATCGATTTGTGTCGCGACTCCGCCCAAATCGTCGTTTATCAGAACCTTTTGGAAGAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.10%	11.50%	0.04%	0.38%	NA
All Indica	2759	81.90%	17.40%	0.04%	0.62%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	82.20%	17.50%	0.37%	0.00%	NA
Indica I	595	94.10%	5.70%	0.00%	0.17%	NA
Indica II	465	78.30%	21.10%	0.00%	0.65%	NA
Indica III	913	77.50%	21.70%	0.00%	0.77%	NA
Indica Intermediate	786	80.00%	19.10%	0.13%	0.76%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0625534713	T -> C	LOC_Os06g42480.1	upstream_gene_variant ; 1954.0bp to feature; MODIFIER	silent_mutation	Average:38.171; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N
vg0625534713	T -> C	LOC_Os06g42470-LOC_Os06g42480	intergenic_region ; MODIFIER	silent_mutation	Average:38.171; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N
vg0625534713	T -> DEL	N	N	silent_mutation	Average:38.171; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625534713	NA	7.33E-06	mr1066	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251